Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resillience

Coral reefs are home to over 2 million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic and other -omics data from different species of reef building corals, the uni-cellular dinoagellates, plus the coral microbiome (where corals have possibly the most complex microbiome yet discovered, consisting of over 20,000 different species), is becoming increasingly available for corals. This new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. This paper summarizes the content of the Bioinformatics of Corals workshop, that is being held as part of PSB 2021. It is particularly relevant for this workshop to occur at PSB, given the abundance of and reliance on coral reefs in Hawaii and the conference’s traditional association with the region

Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck \u3cem\u3ePanopea generosa\u3c/em\u3e following short-term exposure to acidified seawater

While acute stressors can be detrimental, environmental stress conditioning can improve performance. To test the hypothesis that physiological status is altered by stress conditioning, we subjected juvenile Pacific geoduck, Panopea generosa, to repeated exposures of elevated pCO2 in a commercial hatchery setting followed by a period in ambient common garden. Respiration rate and shell length were measured for juvenile geoduck periodically throughout short-term repeated reciprocal exposure periods in ambient (~550 μatm) or elevated (~2400 μatm) pCO2 treatments and in common, ambient conditions, 5 months after exposure. Short-term exposure periods comprised an initial 10-day exposure followed by 14 days in ambient before a secondary 6-day reciprocal exposure. The initial exposure to elevated pCO2 significantly reduced respiration rate by 25% relative to ambient conditions, but no effect on shell growth was detected. Following 14 days in common garden, ambient conditions, reciprocal exposure to elevated or ambient pCO2 did not alter juvenile respiration rates, indicating ability for metabolic recovery under subsequent conditions. Shell growth was negatively affected during the reciprocal treatment in both exposure histories; however, clams exposed to the initial elevated pCO2 showed compensatory growth with 5.8% greater shell length (on average between the two secondary exposures) after 5 months in ambient conditions. Additionally, clams exposed to the secondary elevated pCO2 showed 52.4% increase in respiration rate after 5 months in ambient conditions. Early exposure to low pH appears to trigger carryover effects suggesting bioenergetic re-allocation facilitates growth compensation. Life stage-specific exposures to stress can determine when it may be especially detrimental, or advantageous, to apply stress conditioning for commercial production of this long-lived burrowing clam

Transcriptome Analysis Provides a Blueprint of Coral Egg and Sperm Functions

Background Reproductive biology and the evolutionary constraints acting on dispersal stages are poorly understood in many stony coral species. A key piece of missing information is egg and sperm gene expression. This is critical for broadcast spawning corals, such as our model, the Hawaiian species Montipora capitata, because eggs and sperm are exposed to environmental stressors during dispersal. Furthermore, parental effects such as transcriptome investment may provide a means for cross- or trans-generational plasticity and be apparent in egg and sperm transcriptome data. Methods Here, we analyzed M. capitata egg and sperm transcriptomic data to address three questions: (1) Which pathways and functions are actively transcribed in these gametes? (2) How does sperm and egg gene expression differ from adult tissues? (3) Does gene expression differ between these gametes? Results We show that egg and sperm display surprisingly similar levels of gene expression and overlapping functional enrichment patterns. These results may reflect similar environmental constraints faced by these motile gametes. We find significant differences in differential expression of egg vs. adult and sperm vs. adult RNA-seq data, in contrast to very few examples of differential expression when comparing egg vs. sperm transcriptomes. Lastly, using gene ontology and KEGG orthology data we show that both egg and sperm have markedly repressed transcription and translation machinery compared to the adult, suggesting a dependence on parental transcripts. We speculate that cell motility and calcium ion binding genes may be involved in gamete to gamete recognition in the water column and thus, fertilization

Evolution of Protein-Mediated Biomineralization in Scleractinian Corals

While recent strides have been made in understanding the biological process by which stony corals calcify, much remains to be revealed, including the ubiquity across taxa of specific biomolecules involved. Several proteins associated with this process have been identified through proteomic profiling of the skeletal organic matrix (SOM) extracted from three scleractinian species. However, the evolutionary history of this putative “biomineralization toolkit,” including the appearance of these proteins’ throughout metazoan evolution, remains to be resolved. Here we used a phylogenetic approach to examine the evolution of the known scleractinians’ SOM proteins across the Metazoa. Our analysis reveals an evolutionary process dominated by the co-option of genes that originated before the cnidarian diversification. Each one of the three species appears to express a unique set of the more ancient genes, representing the independent co-option of SOM proteins, as well as a substantial proportion of proteins that evolved independently. In addition, in some instances, the different species expressed multiple orthologous proteins sharing the same evolutionary history. Furthermore, the non-random clustering of multiple SOM proteins within scleractinian-specific branches suggests the conservation of protein function between distinct species for what we posit is part of the scleractinian “core biomineralization toolkit.” This “core set” contains proteins that are likely fundamental to the scleractinian biomineralization mechanism. From this analysis, we infer that the scleractinians’ ability to calcify was achieved primarily through multiple lineage-specific protein expansions, which resulted in a new functional role that was not present in the parent gene

Environmentally-induced parental or developmental conditioning influences coral offspring ecological performance

The persistence of reef building corals is threatened by human-induced environmental change. Maintaining coral reefs into the future requires not only the survival of adults, but also the influx of recruits to promote genetic diversity and retain cover following adult mortality. Few studies examine the linkages among multiple life stages of corals, despite a growing knowledge of carryover effects in other systems. We provide a novel test of coral parental conditioning to ocean acidification (OA) and tracking of offspring for 6 months post-release to better understand parental or developmental priming impacts on the processes of offspring recruitment and growth. Coral planulation was tracked for 3 months following adult exposure to high pCO2 and offspring from the second month were reciprocally exposed to ambient and high pCO2 for an additional 6 months. Offspring of parents exposed to high pCO2 had greater settlement and survivorship immediately following release, retained survivorship benefits during 1 and 6 months of continued exposure, and further displayed growth benefits to at least 1 month post release. Enhanced performance of offspring from parents exposed to high conditions was maintained despite the survivorship in both treatments declining in continued exposure to OA. Conditioning of the adults while they brood their larvae, or developmental acclimation of the larvae inside the adult polyps, may provide a form of hormetic conditioning, or environmental priming that elicits stimulatory effects. Defining mechanisms of positive acclimatization, with potential implications for carry over effects, cross-generational plasticity, and multi-generational plasticity, is critical to better understanding ecological and evolutionary dynamics of corals under regimes of increasing environmental disturbance. Considering environmentally-induced parental or developmental legacies in ecological and evolutionary projections may better account for coral reef response to the chronic stress regimes characteristic of climate change

Short-Term Thermal Acclimation Modifies the Metabolic Condition of the Coral Holobiont

The nutritional symbiosis between coral hosts and photosynthetic dinoflagellates is fundamental to the functioning of coral reefs. Rising seawater temperatures destabilize this relationship, resulting in drastic declines in world-wide coral cover. Thermal history is thought to play an important role in shaping a coral\u27s response to subsequent thermal stress. Here, we exposed Pocillopora damicornis to two thermal acclimation regimes (ambient vs. warm) and compared the effect that acclimation had on the coral holobiont\u27s response to a subsequent seven day heat stress event. We conducted daily physiological measurements at the holobiont level (gross photosynthesis, respiration, host protein content, symbiont density and chlorophyll content) throughout the heating event, as well as cellular-level imaging of 13C-bicarbonate and 15N-nitrate assimilation (using NanoSIMS) at the end of the heat stress event. Thermal acclimation history had a negligible effect on the measurements conducted at the holobiont level during the heat stress event. No differences were observed in the O2-budget between ambient and warm-acclimated corals and only small fluctuations in host protein, symbiont density and chlorophyll content were detected. In contrast, this lack of differential response, was not mirrored at the cellular level. Warm-acclimated corals had substantially higher 13C enrichment in the host gastrodermis and lipid bodies, but significantly lower 15N-nitrate assimilation in the symbionts and the host tissue layers, relative to the ambient-acclimated corals. We discuss potential reasons for the disconnect that occurred between symbiont bicarbonate and nitrate assimilation (in the absence of photosynthetic breakdown) in the warm-acclimated corals. We suggest this represents either a shift in nitrogen utilization, or supply limitation by the host. Our findings raise several interesting hypotheses regarding the role that nitrogen metabolism plays in thermal stress, which will warrant further investigation if we are to understand the acclimatization capacity of the coral holobiont

Digital image processing to detect subtle motion in stony coral

Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community

Metabolomic Shifts Associated with Heat Stress in Coral Holobionts

Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is “coral bleaching,” usually precipitated by prolonged thermal stress. We used untargeted, polar metabolite profiling to investigate the physiological response of the coral species Montipora capitata and Pocillopora acuta to heat stress. Our goal was to identify diagnostic markers present early in the bleaching response. From the untargeted UHPLC-MS data, a variety of co-regulated dipeptides were found that have the highest differential accumulation in both species. The structures of four dipeptides were determined and showed differential accumulation in symbiotic and aposymbiotic (alga-free) populations of the sea anemone Aiptasia (Exaiptasia pallida), suggesting the deep evolutionary origins of these dipeptides and their involvement in symbiosis. These and other metabolites may be used as diagnostic markers for thermal stress in wild coral

Divergent Evolutionary Histories of DNA Markers in a Hawaiian Population of the Coral Montipora capitata

We investigated intra- and inter-colony sequence variation in a population of the dom- inant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2-3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers

MEDFORD: A HUMAN AND MACHINE READABLE METADATA MARKUP LANGUAGE

Reproducibility of research is essential for science. However, in the way modern computational biology research is done, it is easy to lose track of small, but extremely critical, details. Key details, such as the specific version of a software used or iteration of a genome can easily be lost in the shuffle, or perhaps not noted at all. Much work is being done on the database and storage side of things, ensuring that there exists a space to store experiment-specific details, but current mechanisms for recording details are cumbersome for scientists to use. We propose a new metadata description language, named MEDFORD, in which scientists can record all details relevant to their research. Human-readable, easily-editable, and templatable, MEDFORD serves as a collection point for all notes that a researcher could find relevant to their research, be it for internal use or for future replication. MEDFORD has been applied to coral research, documenting research from RNA-seq analyses to photo collections